Description Usage Arguments Details Value Author(s) See Also Examples
Determine the ordered pair of A and B alleles, using the allele information
provided by template
.
1 2 3 | hlaGenoSwitchStrand(target, template,
match.type=c("RefSNP+Position", "RefSNP", "Position"),
same.strand=FALSE, verbose=TRUE)
|
target |
an object of |
template |
a genotypic object of |
match.type |
|
same.strand |
|
verbose |
show information, if TRUE |
The A/B pairs of target
are determined using the information from
template
.
Return a hlaSNPGenoClass
or hlaSNPHaploClass
object consisting of the SNP intersect between target
and
template
.
Xiuwen Zheng
hlaMakeSNPGeno
, hlaMakeSNPHaplo
,
hlaGenoSubset
, hlaHaploSubset
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # load SNP genotypes
data(HapMap_CEU_Geno, package="HIBAG")
summary(HapMap_CEU_Geno)
# A/C A/G C/T G/T
# 136 655 632 141
# import a PLINK BED file
bed.fn <- system.file("extdata", "HapMap_CEU.bed", package="HIBAG")
fam.fn <- system.file("extdata", "HapMap_CEU.fam", package="HIBAG")
bim.fn <- system.file("extdata", "HapMap_CEU.bim", package="HIBAG")
hapmap.ceu <- hlaBED2Geno(bed.fn, fam.fn, bim.fn, assembly="hg19")
summary(hapmap.ceu)
# A/C A/G A/T C/G C/T G/T
# 471 2102 83 134 2046 480
# combine two datasets together
geno <- hlaGenoSwitchStrand(HapMap_CEU_Geno, hapmap.ceu)
summary(geno)
# There are 1564 SNPs in common.
# The allele pairs of 763 SNPs need to be switched.
# A/C A/G C/T G/T
# 136 655 632 141
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